*Transcription Factor database

Dan Jacobson DANJ at JHUHYG.bitnet
Sun Feb 23 15:07:35 EST 1992


A request was made for information about a database of transcription
factors.  Well this database is called TFD (transcription factor
database) and is available from NCBI.  I have included the address of
the ftp site and a listing of the directories which contain tfd files as
well as the readme file for the TFD.

A request was also made for help on archie - since the post was from
Michigan I'll give a US archie site - there are also sites in Canada
(archie's birthplace), Finland, the UK, Israel, Australia ...
To use ARCHIE you may telnet to archie.sura.net and login as archie.
You then can do searches for whatever you want, there is online help.  If
you would like I could send you a help file on ARCHIE.

The other (and better) way that you can access archie is with the use of
a prospero client.  This allows you to send searches to archie (pipe the
results to a file on your system and put it in background if you'd like),
automatically - no telneting, no fuss - just send it off and read the results
when they come back.  To get the client software to do this ftp archie.sura.net
login as anonymous, cd to /pub/archie/client(s?).  It's pretty easy to install.

Hope this helps,


Dan Jacobson
danj at jhuhyg.sph.jhu.edu

=============================================================================
=============================================================================

Host ncbi.nlm.nih.gov

    Location: /pub/ghosh
           FILE -rw-r--r--    4524948  Oct 16 17:41  tfd.testD.cpt.hqx
           FILE -rw-r--r--     899533  Nov 13 15:30  tfdirx.tar.Z
    Location: /repository/TFD/datasets
           FILE -rw-r--r--     847948  Dec 12 18:33  tfdaa
    Location: /repository/TFD/tarfiles
           FILE -rw-r--r--    5279327  Jan 27 22:34  tfd.tar.Z
    Location: /repository/TFD
      DIRECTORY drwxr-xr-x        512  Jan 27 22:19  tfd.ascii
    Location: /repository/TFD/tfd.ascii
           FILE -rw-r--r--       3666  Dec 12 17:09  tfd.dct
    Location: /repository/TFD
      DIRECTORY drwxr-xr-x        512  Jan 27 22:21  tfd.asn1
    Location: /repository/TFD/tfd.asn1
           FILE -rw-r--r--    7495648  Jan 27 22:22  tfd.asn
           FILE -rw-r--r--       3107  Dec 16 17:14  tfd.asnspec


=========================================================================
================================README===================================


**************************************************************************
*                                                                        *
*                             COPYRIGHT NOTICE                           *
*                                                                        *
* This software/database is "United States Government Work" under the    *
* terms of the United States Copyright Act.  It was written as part of   *
* the author's official duties as a Government employee and thus cannot  *
* be copyrighted.  Restrictions cannot be placed on its present or       *
* future use.                                                            *
*                                                                        *
* Although all reasonable efforts have been taken to insure the accuracy *
* and reliability of the software and data, the author(s), the National  *
* Library of Medicine (NLM) and the U.S. Government do not and cannot    *
* warrant the performance or results that may be obtained by using this  *
* software or data.  The author(s), the NLM and the U.S. Government      *
* disclaim all warranties, expressed or implied, as to performance,      *
* merchantability or fitness for any particular purpose.                 *
*                                                                        *
* In any work or product derived from this material, proper attribution  *
* of the author as the source of the software or data would be           *
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**************************************************************************




February 14, 1992
---------------------------------------------------------------------------


I.   Release Notes:

This file only contains information specific to the 4.0 and
4.2 releases.  Users who are unfamiliar with TFD are suggested
to peruse the contents of README files of previous releases,
which are contained in the "Release-Notes" subdirectory.

II.  Number of records per table:

This (4.2) release contains 1658, 929, 434, 1511, and 1887 records
for the clones, domains, factors, polypeptides, and sites tables,
respectively.  The methods, n_pointers, references, and x_pointers
tables contain 34, 2552, 5726, and 4872 records respectively.

III. Database structure:

The following changes in database structure have occurred between
releases 3.0 and 4.2:


Table           Field           Description
---------------------------------------------------------------------------

methods                         New TFD table containing codes for
                                experimental methods, corresponding
                                (in release 4.1) to information
                                contained in the sites.method field

methods         full            experimental method
                tfdcode         two-letter code used by TFD

references      medline         changed to 'uid'

clones          tfd_id          changed to 'clone_id'
domains         tfd_id          changed to 'domain_id'
factors         tfd_id          changed to 'factor_id'
polypeptides    tfd_id          changed to 'polypep_id'
sites           tfd_id          changed to 'site_id'

sites           locat_ref       new field containing reference point
                                for coordinates contained in the
                                sites.location field

n_pointers      table1          new field containing the name of the
                                table for the id referenced in id_1
                tfdid1          changed to 'id_1'
                table2          new field containing the name of the
                                table for the id reference in id_2
                tfdid2          changed to 'id_2'

x_pointers      tfd_table       new field containing the name of the
                                TFD table pointed to in an x_pointers
                                entry
                tfdentry        changed to 'tfd_id'



III.  Software:

The following public domain software packages can be
used with TFD:

Dynamic, a SITES analysis software tool developed for a UNIX
operating system, which can be obtained from the the MBCRR.
For this product contact Temple Smith (tsmith at darwin.bu.edu).

Signalscan, a SITES analysis software tool developed for use
on a PC, Macintosh, UNIX, or VMS system.  For this product
please contact D Presteridge (danp at beagle.colorado.edu).

SITES dataset files for use with these and other software
packages can be found in the directory "datasets".


IV.   Reference:

The following references may be consulted for a background
and general description of this database:

Ghosh, D. (1990)  A Relational Database of Transcription Factors.
Nucleic Acids Research 18:  1749-1756.

Ghosh, D. (1991)  New developments of a Transcription Factors
Database.  Trends in Biochemical Sciences 16:  455-457.


V.  Help/Further Information:

The following addresses can be used for help requests, mailing
list requests and general questions:


Email (internet) address                Purpose
----------------------------------------------------------------------------


tfdhelp at ncbi.nlm.nih.gov                TFD-related technical help requests

tfdinfo at ncbi.nlm.nih.gov                Address for messages or questions
                                        directed to the TFD users community.

tfdinfo-request at ncbi.nlm.nih.gov        Request for subscrtiption to the
                                        TFDINFO users mailing list.


----------------------------------------------------------------------------

David Ghosh
National Center for Biotechnology Information
NLM, NIH
Bethesda, MD  20894  USA

Internet address:  ghosh at ncbi.nlm.nih.gov

----------------------------------------------------------------------------




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